- phenixbb - phenix-online.org

Refinement using a homolog as a reference
by Joshi, Amar (Dr.) 25 Jul '13

25 Jul '13

Hi, I am refining ligand-protein complexes at 3.2Å dataset with a human protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85% favoured, 4.5% disallowed. The structure of a yeast homolog has been deposited at 2.4Å resolution. The yeast structure contains additional loops but is ~55% identical to the human protein. The overall conformation between the homologs is very similar. Can I use this as a reference model? Should I prune the reference model? Will different numbering schemes affect the refinement? Many thanks, Amar

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Re: [phenixbb] Linux distribution question: who needs the FC3 build?
by Nathaniel Echols 25 Jul '13

25 Jul '13

On Wed, Jul 24, 2013 at 2:56 PM, Edward A. Berry <BerryE(a)upstate.edu> wrote: > Would that be the end of support for 32-bit linux? Or would you build > i686 version on a later version? (Or is it possible to run 64 bit > executable on 32- bit operating systems with some kind of compatibility > libraries and 64-bit capable hardware?) > > I have one Fc8 32 bit machine which I don't want to upgrade, but I don't > really need to run phenix on it. Just to clarify: we will continue distributing 32-bit Linux indefinitely (although probably on fewer platforms than 64-bit), and we will at least support Fedora 8 at a minimum for a while, since our most important development system is still running it. The question is really related to how ancient a distribution we need to support, and what scenarios are especially difficult for binary cross-compatibility. -Nat

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calculate map from ensemble refinement
by Bard, Joel 23 Jul '13

23 Jul '13

Hi- I ran phenix.ensemble refinement which worked very nicely but crashed during map output. I think this was my fault for using a parameter file that had map_type = None (I didn't look and assumed the default was reasonable). I would like to calculate maps after the fact. Is there a way to run the map calculation on the output ensemble pdb file and reflection data? I tried phenix.maps which choked on the huge ensemble. Thanks, Joel

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Group ADP refinement
by joseph Lyons 23 Jul '13

23 Jul '13

Dear phenixbb. I am currently running phenix 1.8.2-1309. My goal is to use group ADP with 2 b-factors per residue for the protein and individual b-factors for solvent. However, this does not seem to be working even though the system seems to recognise what I want to do. The refinement output gives what looks like individual b-factor refinement... ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4048 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 127 aniso = 0) group_adp = True (3921 atoms in 967 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False In troubleshooting it appears that with Group ADP with 2 b-factors per residue, the solvent B-factors are not being refined, i.e., remaining at the Wilson B that I set previously. For Group ADP with 1 b-factors per residue - everything appears to refine OK. Any help would be greatly appreciated, Regards, Joe

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Re: [phenixbb] How do I turn off sidechain rotamer fitting? (Pavel Afonine)
by Joseph Noel 23 Jul '13

23 Jul '13

Dear Pavel, To clarify, in the latest nightly build, 1435, do you have to click on real space refinement to carry out side chain rotamer fitting? If you just refine xyz I assume side chain rotamer fitting is not enabled, correct? Joe Noel ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Re: [phenixbb] Phenix "hangs" on a Mac?
by Joseph Noel 23 Jul '13

23 Jul '13

Hi Nat, Will replicate and send you the information. Its unrelated to Ramachandran restraints as it occurs intermittantly when doing just regular tasks. I can always tell early as it never seems to get past the first steps of the refinement protocol - in essence - it never starts xyz refinement. Just sits there. I abort and restart and it then goes fine. I'm running Mac OSX 10.8.4 Joe ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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Post-doc position for SAXS at the MAX IV Laboratory
by Marjolein Thunnissen 23 Jul '13

23 Jul '13

The MAX IV laboratory in Lund has opened a position for a Postdoctoral fellow to strengthen the biological SAXS environment at the current SAXS beam line. The position will be for two years and is embedded in the BIOSTRUCT-X EU program. Full information of the position is available at: http://admin.lu.se/o.o.i.s?id=22598&Dnr=554436&Type=E as well as who to contact for more information. Information about the MAX IV laboratory can be obtained at www.maxlab.lu.se<http://www.maxlab.lu.se> . best regards Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Phenix "hangs" on a Mac?
by Joseph Noel 22 Jul '13

22 Jul '13

Has anyone had a problem when using Phenix refine through the GUI on a Mac wherein the program after hitting Run locally starts but then hangs without proceeding? Seems to happen to me about one out of five times I run refine and always hangs when I experiment with ramachandran restraints for only a portion of the polypeptide chain. I've tried letting things alone for several hours and nothing happens. I can abort and then often resubmit and it then runs fine (except for rama restraints). I've found this happens with both nightly builds and stable releases. I am currently running the latest nightly build 1439. ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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On Mac two separate installations?
by Joseph Noel 22 Jul '13

22 Jul '13

Does one have to install both the GUI and command line installers on a Mac if one wants to have the option of running using the command line (for command line only options in nightly builds) and the GUI? ______________________________________________________________________________________ Joseph P. Noel, Ph.D. Arthur and Julie Woodrow Chair Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Publications & Citations: http://scholar.google.com/citations?user=xiL1lscAAAAJ Homepage Salk: http://www.salk.edu/faculty/noel.html Homepage HHMI: http://hhmi.org/research/investigators/noel.html ______________________________________________________________________________________

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mr_rosetta pause & resume
by Karolina Michalska 22 Jul '13

22 Jul '13

Hello everybody, Is there a way to pause an mr_rosetta run and resume it with a different number of processors? Thanks, Karolina

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Registration open: "The Future of Microfocus Protein Crystallography"
by Marjolein Thunnissen 22 Jul '13

22 Jul '13

Dear all, I would like to remind you on a workshop on "The Future of Microfocus Protein Crystallography" which will take place at the MAX IV User meeting on the 24th and the 25th of September, 2013, in Lund, Sweden. Recent developments within protein crystallography methods in combination with the possibilities offered by the new upcoming synchrotron sources such as the MAX IV 3 GeV storage ring make possible exciting new ways of carrying out research within structural biology. Small microfocus beamlines with a very high flux and increased coherence will make new types of experimentation possible. The scientific possibilities will be highlighted through a series of talks by experts showing the impact of the new type of X-ray sources and microfocus beamlines on research within structural biology. The new generation of microfocus beamlines will also set a high demand on instrumentation and suitable software. For example, data collection will potentially be very fast (in milliseconds) and radiation damage will allow only a limited amount of data to be collected from each sample. New technical solutions for sample handling and presentation, data processing methods and more will be needed for these types of experiments, and these will also be presented and discussed at the workshop. Confirmed speakers include David Stuart, Daniel Wacker, Simone Weynand, Jens Preben Morth, Tove Sjögren, Richard Neutze, Janet Smith, Alke Meentz, Alexei Soares, Thomas White, Luca Jovine and Clemens Schulze-Briese The workshop is part of a process to obtain an updated proposal for the possible Phase 2b beam line MicroMAX at the upcoming new 3 GeV storage ring of MAX IV in Lund. This workshop should give the user community an opportunity to explore the scientific possibilities of a new generation of microfocus beam lines, but also it will give them the chance to contribute with specific input on their own experimental demands on the beam line. The workshop is part of the MAX IV laboratory user meeting, but there is no requirement to be a user of the facility and all that are interested are welcome . Registration is through the user meeting website: https://indico.maxlab.lu.se/indico/conferenceDisplay.py?confId=0 . The registration fees are 2000 SEK for academics and 700 SEK for junior scientists. Registration fees include all lunches and the conference dinner. Further information on this workshop can be found at https://www.maxlab.lu.se/node/1609 and for the MAX IV user meeting at https://www.maxlab.lu.se/um13 . For the organisers, Richard Neutze, Gunter Schneider and Gregers Rom Andersen Marjolein Thunnissen ________________________________________________________________________ Marjolein Thunnissen Phone +46-(0)76-632 0417 Associate Professor Fax +46-(0)46-22 24692 Dept of Biochemistry and Structural Biology, Lund University http://www.mps.lu.se<http://www.mps.lu.se/> PO-Box 124 S-221 00 Lund, Sweden Scientific coordinator MX (The MAX IV Laboratory): I911 and BioMAX ________________________________________________________________________

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Fo-Fo map
by Xiang Li 22 Jul '13

22 Jul '13

Hi everyone, I am working on two datasets of the similar crystal design. In one of the datasets, there is an extra guest protein (might be considered as a ligand) docked in one unit cell. The two crystals have very similar unit cell size and same symmetry. I want to calculate the Fo-Fo map to see whether I could figure out where the protein is. But I got error says the symmetry of the two datasets are not the same. I have never used the "isomorphous difference map" in GUI before. Can anyone help me to figure out where I did wrong please? I have attached the mtz file that I want to compare. Btw, if the protein is not very rigidly linked with the crystal framework (~2 free residues linkage), am I supposed to see the density of the protein? Or are there any better ways for me to identify the protein? Thanks for your kind help! Sincerely, Xiang

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ADP refinement of cysteinesulfonic acid
by Phillip Steindel 16 Jul '13

16 Jul '13

Hi all- I have a 1.5 Angstrom structure with two cysteines that appear to have oxidized to cysteinesulfonic acid (OCS). I replaced the cysteines in coot, then ran refine with individual and anisotropic ADPs, but the ADPs don't appear to be refining for those residues. The hydrogens are all at 24,and the non-hydrogens are all at 20. I'm running 1.8.2-1309. Thanks, Phillip Steindel Theobald Lab Brandeis University

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cis peptide question
by Edward A. Berry 16 Jul '13

16 Jul '13

I have a cis-peptide in my structure. Phenix recognizes it and .geo file shows this is restrained to 0*: dihedral pdb=" CA ALA A 401 " pdb=" C ALA A 401 " pdb=" N SER A 402 " pdb=" CA SER A 402 " ideal model delta harmonic sigma weight residual 0.00 -1.58 1.58 0 5.00e+00 4.00e-02 1.00e-01 However in statistics printed with the output pdb, I have at least one dihedral that is flagged as off by about 180*: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 DIHEDRAL : 12.902 168.987 3277 ^^^^^^^ Could this be my cis peptide, or do I have a really bad dihedral somewhere else?

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How do I turn off sidechain rotamer fitting?
by Owen Pornillos 15 Jul '13

15 Jul '13

I'm using one of the nightlies - dev 1427. It's not doing very well in combination with NCS. Or what is the most recent nightly that does not have this feature? Many thanks, Owen

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Kicked difference maps
by Ho Leung Ng 13 Jul '13

13 Jul '13

Hi, I am finding that features in kicked difference maps (mFo-DFc) have very different scaling compared to the standard difference maps. For example, a blob that appears in the standard map at 3 sigma might not appear in the kicked map until 5.5 sigma. Is this correct functioning? In contrast, features in the kicked and standard 2mFo-DFc maps are comparable in scale. Thank you, Ho Ho Leung Ng University of Hawaii at Manoa Assistant Professor, Department of Chemistry hng(a)hawaii.edu

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problem with alternate conformations
by George Phillips 11 Jul '13

11 Jul '13

I am trying to adapt my old CNS scripts to to multiple conformer refinements in Phenix, i.e. up to 20 copies of each entire chain. I seem to be OK with up to three copies of the whole chain, but when I try four or more I seem to be in an infinite loop in the 'reduce' phase of a refinement. 3 copies runs in less than hour, even with torsion simulated annealing, with four even overnight the program just runs 'reduce for hours and hours'. This happens on the standard release and development version 1422. Is there some way to turn off hydrogens as a work around? Test files available on request. : ) Thanks for any help! George George N. Phillips, Jr. Ralph and Dorothy Looney Professor Department of Biochemistry and Cell Biology Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 http://www.bioc.rice.edu/

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2014 Gordon Research Conference and Research Seminars on Diffraction Methods in Structural Biology
by Anastassis Perrakis 11 Jul '13

11 Jul '13

Dear all, In a bit more than a year from now, we will be running the Gordon Research Conference on Diffraction Methods in Structural Biology, this time preceded for the first time by a two-day Gordon Research Seminar, exclusively for young scientists and a few mentors. http://www.grc.org/programs.aspx?year=2014&program=diffrac http://www.grc.org/programs.aspx?year=2014&program=grs_diff We are in the process of inviting the right people to make the schedule as exciting and inviting as possible, hoping we will be able to attract a diverse, enthusiastic, and motivated crowd! At this stage, we would like to ask you for ideas for 1. Specific subjects that are emerging and you would like to see covered, to make it worth your time to join us! 2. Specific people that would be excellent speakers, that would make you attend the Research Conference! 3. Specific people that would be great mentors, that would make you attend the Research Seminars! Many thanks from the team (but please send all replied to me!) Tassos Perrakis (GRC chair), Eddie Snell (GRC vice chair), Jeff Headd (GRS chair) and Maike Bublitz (GRS assoc. chair)

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parallel phenix.phaser on SGE cluster
by L. Costenaro (IBB) 11 Jul '13

11 Jul '13

Hello, I am trying to run phaser in a SGE cluster (qsub) using multiple proc (either phenix.phaser from the command line or phaser-MR from the GUI), but the jobs do not parallelize. When I run the phaser-MR locally (same executable) it does parallelize (multiple python threads). Any help , advice would be welcome. Best regards, Lionel

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Location of Gaussian factors for ED calculation
by Schubert, Carsten [JRDUS] 10 Jul '13

10 Jul '13

Hi, Were in the phenix package can I find the Gaussian factors (scattering table) for calculating the isotropic ED distribution at a given radius of r. I just need that for an illustration. Even better of you could already point me to some plots. Nothing I found online so far was suitable. Thanks Carsten

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: Post-doctoral position in structural biology (Paris, France)
by Benas Philippe 10 Jul '13

10 Jul '13

POST-DOCTORAL POSITION IN STRUCTURAL BIOLOGY (PARIS, FRANCE) . A postdoctoral position is available in the group of Dr. Carine Tisne at the Laboratory of Biological Crystallography and NMR of the University Paris Descartes, jointly with the group of Dr. Ciaran Condon at the Laboratory of Microbial Gene Expression (CNRS UPR9073) of the Institut de Biologie Physico-Chimique. We are studying the structure, function and folding of RNA and their complexes using NMR spectroscopy and X-ray crystallography, together with complementary biophysical methods. The postdoctoral research project focusses on the processing of the 5 and 3 ends of 5S rRNA in Gram-positive bacteria using solution NMR and X-ray crystallography as the main techniques. An integral part of our projects is the use and development of state-of-the-art preparative, biochemical and NMR techniques. . Interested candidates should hold a Ph.D. in Biochemistry, Biophysics or Structural Biology. Expertise in NMR spectroscopy and/or X-ray crystallography is mandatory. The successful candidate should be highly motivated, creative and capable of independent research in a two-team environment (10 minute walk between labs). The position is for a two-year term contract (one year in each team). We offer an exciting and enthusiastic work environment together with a stimulating location at the center of Paris (close to Jardin du Luxembourg). Facilities for structural biology include 600 MHz Bruker spectrometer equipped with cryoprobe. A new 700 MHz spectrometer will be installed in 2014. We also have access to high-field NMR spectrometers through the French TGIR and regular access to synchroton beamtime at either the ESRF or SOLEIL as Beam Time Allocation Group member. The ideal start date for the position would be October 2013. . Applications and informal queries about the labs and research projects should be directed by email to Carine Tisne (carine.tisne(a)parisdescartes.fr) or Ciaran Condon (condon(a)ibpc.fr[1]). Applications must include a letter of motivation summarizing current and future research interests, a CV, list of publications and letters of recommendation from at least two references. . ------------------------- PHILIPPE BENAS, PH.D. X-ray diffraction and computing facilities manager Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS E-mails: philippe.benas(a)parisdescartes.fr, philippe_benas(a)yahoo.fr URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18 ------------------------- "We do know nothing ! But tomorrow is another day ! ;-) " Liens: ------ [1] mailto:[email protected]

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give-up-quick Phaser in Rosetta
by Morten Grøftehauge 10 Jul '13

10 Jul '13

Dear Phenixbb, I was wondering if there was any way of getting Rosetta to give up easily and move on to another search model? Say I have 20 or more equally awful search models. I think there's a possibility that one of them will knock it out of the park (i.e. TFZ > 8). But even if I have Phaser set to fast search I will end up with an exhaustive search because the search models are so bad. fast_search_mode= True Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent search_down_percent= 25 Used if fast_search_mode=True. Run phaser with selection_criteria_rot_value and then if no obvious solution, repeat with cutoff lowered by search_down_percent If I set search_down_percent to 75 does this mean that Phaser will give up easily and move on to the next model? Is this a terrible strategy CPU-time-wise? I am of course aware that search_down_percent is much more likely to give me the right solution for a given model but in this case there are just so many possible search models. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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inconsistent Rwork/Rfree in outputs
by Michael Thompson 09 Jul '13

09 Jul '13

Hello All, I am getting an output from phenix.refine that is somewhat confusing to me. I have a log file that seems to be reporting inconsistent values for the final Rwork and Rfree. The last line of my log file says: Final R-work = 0.1815, R-free = 0.1912 However, when I check the pdb file from phenix.refine, I see: REMARK Final: r_work = 0.1799 r_free = 0.1952 bonds = 0.012 angles = 1.315 In the log file, I get the following table, which seems to agree with what is in the pdb file. R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.1971 0.1916 1.408780e-01 1.965297e-01 1_bss: 0.1971 0.1916 1.508155e-01 2.122150e-01 1_ohs: 0.1971 0.1916 1.447084e-01 2.026856e-01 1_xyz: 0.1928 0.2001 1.348543e-01 2.162596e-01 1_adp: 0.1929 0.2134 1.006068e-01 1.652532e-01 1_occ: 0.1928 0.2127 9.708801e-02 1.642701e-01 2_bss: 0.1784 0.1978 1.001979e-01 1.536656e-01 2_ohs: 0.1786 0.1982 1.146147e-01 1.876601e-01 2_xyz: 0.1777 0.1959 1.187570e-01 1.899659e-01 2_adp: 0.1952 0.2001 1.109064e-01 1.588435e-01 2_occ: 0.1952 0.1995 1.059382e-01 1.580417e-01 3_bss: 0.1831 0.1888 1.066004e-01 1.508888e-01 3_ohs: 0.1833 0.1890 1.217008e-01 1.855605e-01 3_xyz: 0.1824 0.1897 1.256200e-01 1.855714e-01 3_adp: 0.1876 0.2039 1.027854e-01 1.533022e-01 3_occ: 0.1877 0.2042 9.739524e-02 1.525993e-01 4_bss: 0.1770 0.1931 9.830779e-02 1.515598e-01 4_ohs: 0.1772 0.1933 1.132096e-01 1.824877e-01 4_xyz: 0.1775 0.1933 1.179076e-01 1.860704e-01 4_adp: 0.1911 0.2005 1.074584e-01 1.546149e-01 4_occ: 0.1909 0.1997 1.023003e-01 1.530269e-01 5_bss: 0.1805 0.1895 1.034638e-01 1.506407e-01 5_ohs: 0.1807 0.1895 1.185810e-01 1.828381e-01 5_xyz: 0.1803 0.1899 1.244219e-01 1.801964e-01 5_adp: 0.1893 0.2019 1.072974e-01 1.503622e-01 5_occ: 0.1893 0.2023 1.016701e-01 1.492730e-01 6_bss: 0.1792 0.1915 1.021896e-01 1.490341e-01 6_ohs: 0.1794 0.1915 1.174694e-01 1.798680e-01 6_xyz: 0.1804 0.1926 1.224254e-01 1.830383e-01 6_adp: 0.1952 0.2015 1.118187e-01 1.549205e-01 6_occ: 0.1950 0.2017 1.063759e-01 1.538692e-01 7_bss: 0.1842 0.1922 1.076805e-01 1.529198e-01 7_ohs: 0.1845 0.1918 1.227818e-01 1.857086e-01 7_xyz: 0.1846 0.1917 1.292627e-01 1.856928e-01 7_adp: 0.1885 0.2042 1.071531e-01 1.532154e-01 7_occ: 0.1885 0.2044 1.012764e-01 1.524448e-01 7_bss: 0.1797 0.1952 1.353649e-01 1.556126e-01 7_ohs: 0.1799 0.1952 1.353649e-01 1.556126e-01 I'm wondering why this last line of the log file isn't consistent with the other values that are being reported for R/Rfree? Which numbers should I believe? Thanks, Mike -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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GUI admin issues
by Yarrow Madrona 09 Jul '13

09 Jul '13

Hello, I have a couple of GUI related questions 1. We recently moved all of our data from one hard drive to another. However, we do not know how to change the directory for all of our projects. The directory is similar but the hard drive is now called tp3home instead of tp2home. We found a .phenix directory that has a file with a list of projects and directories. We updated the directories but this did not make a difference in the GUI. 2. Is there a quick way to specify which ligand or amino acid to remove in the GUI with doing simmulated annealing or better to do manually? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] omit map for protein-DNA complex
by Wei Shi 09 Jul '13

09 Jul '13

Hi guys, With the help of Tom and Nat, I fixed the errors in my pdb file and could generate the simulated annealing omit map for the protein-DNA complex structure! But when I opened resolve_composite_map.mtz and *_ed.pdb in Coot, I could only see one monomer of the protein in Coot. It should be two dimers of the protein plus two pieces of DNA. And when I opened the *_ed.pdb in pymol, it showed the right thing: two dimers of the protein plus two pieces of DNA. It seems that something in *_ed.pdb file is not recognized by Coot. I don't know whether any of you had this before and would have any suggestions for me. When I opened *_ed. pdb with text file and found out that the word "break" is used instead of "ter" between different chains, so I replaced all "break" with "ter", but this didn't help.... Thank you so much! Best, Wei On Wed, Jul 3, 2013 at 10:36 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: > Hi Nat and Tom, > Thank you so much for your help! I don't know why those C7 atoms are > there.... I just added some nucleotides manually using coot to fit the > density. I am going to delete those C7 atoms in DA and see whether that > would help. Thank you guys so much! > > Best, > Wei > > On Tue, Jul 2, 2013 at 5:22 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > >> Okay, this makes sense. Wei, are you trying to model methylated DNA, >> or are those C7 atoms there by accident? >> >> -Nat >> >> On Tue, Jul 2, 2013 at 12:11 PM, Terwilliger, Thomas C >> <terwilliger(a)lanl.gov> wrote: >> > Hi Nat, >> > I think it was the input file. Here is a little piece of it: >> > >> > ATOM 3157 P DA E 8 -56.682 44.723-118.292 1.00 37.45 >> P >> > ATOM 3158 C5' DA E 8 -54.313 44.743-117.204 1.00 40.32 >> C >> > ATOM 3159 O5' DA E 8 -55.729 44.807-117.015 1.00 38.38 >> O >> > ATOM 3160 C4' DA E 8 -53.551 44.795-115.886 1.00 35.58 >> C >> > ATOM 3161 O4' DA E 8 -53.433 46.172-115.429 1.00 32.68 >> O >> > ATOM 3162 C3' DA E 8 -54.164 44.027-114.709 1.00 30.30 >> C >> > ATOM 3163 O3' DA E 8 -53.117 43.597-113.848 1.00 30.92 >> O >> > ATOM 3164 C2' DA E 8 -54.997 45.106-114.029 1.00 18.46 >> C >> > ATOM 3165 C1' DA E 8 -53.974 46.233-114.120 1.00 19.87 >> C >> > ATOM 3166 N1 DA E 8 -52.933 50.956-112.506 1.00 4.27 >> N >> > ATOM 3167 C2 DA E 8 -52.179 49.849-112.633 1.00 5.31 >> C >> > ATOM 3168 N3 DA E 8 -52.515 48.630-113.069 1.00 3.59 >> N >> > ATOM 3169 C4 DA E 8 -53.816 48.619-113.401 1.00 5.26 >> C >> > ATOM 3170 C5 DA E 8 -54.722 49.662-113.344 1.00 5.31 >> C >> > ATOM 3171 C6 DA E 8 -54.237 50.894-112.863 1.00 4.84 >> C >> > ATOM 3172 N6 DA E 8 -55.010 51.981-112.750 1.00 5.38 >> N >> > ATOM 3173 C7 DA E 8 -56.909 56.086-110.227 1.00 2.18 >> C >> > ATOM 3174 N7 DA E 8 -55.973 49.258-113.789 1.00 6.11 >> N >> > ATOM 3175 C8 DA E 8 -55.803 47.992-114.102 1.00 7.27 >> C >> > ATOM 3176 N9 DA E 8 -54.525 47.556-113.888 1.00 8.54 >> N >> > ATOM 3177 OP1 DA E 8 -56.215 43.588-119.122 1.00 44.46 >> O >> > ATOM 3178 OP2 DA E 8 -58.094 44.785-117.853 1.00 32.00 >> O >> > >> > Notice the C7 that is not attached to anything and is not normally part >> of a DA nucleotide. >> > -Tom T >> > >> > On Jul 2, 2013, at 1:07 PM, Nathaniel Echols wrote: >> > >> >> On Tue, Jul 2, 2013 at 9:03 AM, Wei Shi <wei.shi118(a)gmail.com> wrote: >> >>> Below is the error message I got when I ran a plain refinement of the >> same >> >>> PDB file and data file. I also ran phenix.ready-set of the PDB file >> using >> >>> default setting (add hydrogen to model if absent, et al) and generate >> a >> >>> updated PDB file and ran refine again, but still got the same error >> message >> >>> as below: >> >> >> >> This sounds like a bug. Could you please email us off-list with the >> >> PDB file and any existing restraints? (We can fake the data for >> >> testing purposes.) >> >> >> >> -Nat >> > >> > >

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